Search Results for "annotation" - Page 3
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Showing 81 open source projects for "annotation"
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lr2rmats
Long read to rMATS
lr2rmats is a Snakemake-based light-weight pipeline which is designed to utilize both third-generation long-read and second-generation short-read RNA-seq data to generate an enhanced gene annotation file. The newly generated annotation file could be provided to rMATS for differential alternative splicing analysis. More information can be found at https://sourceforge.net/p/lr2rmats/wiki/Home/ -
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SmartMuseum
Software for work with Corpus of Everyday life history Sources
...Corpuses of everyday life history sources are being collected in many museums and document archives. In this project, we consider the problem of creating software infrastructure for collaborative semantic annotation, information relation, and personalized access to corpus of everyday life history sources. Project financially supported from Department for Humanities of Russian Fund for Basic Research according to project # 16-01-12033. Authors: Vdovenko A., Marchenkov S., Petrina O., Korzun D. -
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WikiSQL
A large annotated semantic parsing corpus for developing NL interfaces
A large crowd-sourced dataset for developing natural language interfaces for relational databases. WikiSQL is the dataset released along with our work Seq2SQL: Generating Structured Queries from Natural Language using Reinforcement Learning. Regarding tokenization and Stanza, when WikiSQL was written 3-years ago, it relied on Stanza, a CoreNLP python wrapper that has since been deprecated. If you'd still like to use the tokenizer, please use the docker image. We do not anticipate switching... -
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MethyMer
Design of specific primer combinations for bisulfite sequencing
...It also incorporates TCGA CpG methylation (microarrays) and gene expression (RNA-Seq) data, as well as methylation-expression correlation analysis results for 20 human cancer types. ENCODE genome regions annotation data are also integrated in MethyMer -
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BioC
We describe a simple XML format to share text documents and annotation
A minimalist approach to share text documents and data annotations. Allows a large number of different annotations to be represented. Project files contain: - simple code to hold/read/write data and perform sample processing. - BioC-formatted corpora - BioC tools that work with BioC corpora BioC goals - simplicity - interoperability - broad use - reuse There should be little investment required to learn to use a format or a software module to process that format. We are... -
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ncPRO-seq
Non-Coding RNA PROfiling from sRNA-seq
ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. ############# Docker version : download and run Dockerfile (go in "Files" section) ############# GitHub : https://github.com/jbrayet/ncpro-seq -
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Scaffold_Builder
Combining de novo and reference-guided assembly with Scaffold_builder
...Gaps are filled with N's and small overlaps are aligned with Needleman–Wunsch algorithm and the consensus created with IUPAC codes. Scaffold_builder can help in the assembly and annotation of genomes by revealing what is missing and allowing targeted sequencing to close those gaps. (c) Silva GG, Dutilh BE, Matthews TD, Elkins K, Schmieder R, Dinsdale EA, Edwards RA. Please cite: "Combining de novo and reference-guided assembly with Scaffold_builder", Source Code for Biology and Medicine 2013. -
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ChIP-RNA-seqPRO
ChIP-RNA-sequencing-processing (ChIP-RNA-seqPRO)
ChIP-RNA-seqPRO: A strategy for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing sites. Runnable python scripts packaged together with customized annotation libraries, demo data input and README guide. 9/26 : v1.1 Updated MAIN_IV to debug error thrown by python pandas no longer supporting 'subset'. This code will no longer be actively maintained/updated here. A cloud-based resource for comparative analysis of epigenetic, sequence variation, and expression datasets is now available. ... -
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Squere is a prokaryote genome annotation user-friendly software, with easy installer and graphical interface.
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mwetoolkit
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit3/
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit3/ The Multiword Expressions toolkit aids in the automatic identification and extraction of multiword units in running text. These include idioms (kick the bucket), noun compounds (cable car), phrasal verbs (take off, give up), etc. Even though it focuses on multiword expresisons, the framework is quite complete and can also be useful in any corpus-based study in computational linguistics. The mwetoolkit can be... -
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mitoMaker
mitoMaker - a mitochondria assembly and annotation script
mitoMaker is a pipeline script developed to simplify the assembly and automatic annotation of mitochondrial genomes, based on raw NGS reads and an optional target reference. mitoMaker calls well known assemblers and algorithms, such as SOAPdenovo, MIRA and blast+ and parses their results providing easily readable outputs, such as FASTA, GENBANK, SEQUIN, PNG and others. General pipeline: 1-iterative De Novo assembly, with different k-mer values, trying to assemble a build that matches a target mitochondrial genome given. 2-searches for all mitochondrial gene features and circularization. 3-stores the best result found. 4-uses the best assembly as backbone for a reference based assembly, using MIRA and MITObim, trying to extend the mitogenome and close gaps. 5-annotates the best assembly, identifying the start and end position of each and every feature. 6-creates a folder with all the results (PNG, GENBANK, FASTA, SEQUIN, CAF, MAF and a stats logfile). -
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...IMPACT utilizes multi-reads in calling peaks and provides users with high-confidence peaks. In addition, IMPACT provides a completely integrated pipeline which produces downstream analysis results such as motif discovery and peak-to-gene annotation.
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SeqSelector
Tools to select sequences for capture enrichment of next-gen libraries
...The scripts require no knowledge of programming, and can be applied to genome sequences of model or non-model species. We suggest a workflow in which genes of interest are first identified from previous studies and publicly available datasets of functional gene annotation. Once a list of candidate genes has been identified, their sequences are selected from the reference genome. These sequences are used as a query during a BLAST search of the unannotated genome of a non-model species, and then the corresponding sequences are returned, which can be used to design baits for hybridization-based sequence capture. -
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Russian morphology tagger. Parses text(s) and output xml representation of text(s) with grammatical annotation.
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pyMantis is a data-management system for (systems) biology build on the web2py framework. It features: tree based file explorer, relational db table wizzard with automated creation of user interfaces, internal and external access management, wiki, ..
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Genomic Binding Sites Analyser (BiSA)
Genomic Region Archiving and Binding Sites Analysis (BiSA)
...BiSA can also annotate binding regions of interest with nearby genes. The results of overlap analysis can be imported into the Knowledge Base, allowing them to go into downstream analysis and independent annotation. A Venn diagram tool is also integrated into the software to allow users to visualize overlap results. -
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Donatus is an on-going project consisting of Python, NLTK-based tools and grammars for deep parsing and syntactical annotation of Brazilian Portuguese corpora. It includes a user-friendly graphical user interface for building syntactic parsers with the NLTK, providing some additional functionalities.
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NotaBene RDF Annotation Tool is a wxPython graphical user interface. Its primary purpose is to ease the use of RDF to manually annotate electronic XML editions of left-to-right-written texts. It allows multiple views of the annotated document.
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CDSbank
multi-sequence extraction, filtering & formatting
CDSbank is a database that stores both the protein-coding DNA sequence (CDS) and amino acid sequence for each protein annotated in Genbank. CDSbank also stores Genbank feature annotation, a flag to indicate incomplete 5’ and 3’ ends, full taxonomic data, and a heuristic to rank the scientific interest of a species. This rich information allows fully automated data set preparation with a level of sophistication that meets or exceeds manual processing. Defaults ensure ease of use for typical scenarios while allowing great flexibility when needed. ... -
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A bioinformatics tool for the annotation and tag-counting of next-gen Illumina Solexa datasets. TASE works with CASAVA 1.0 builds, providing annotation, tag counts and visualization in a rapid manner.
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TerraLook provides access to satellite images for users that lack prior experience with remote sensing or Geographic Information System (GIS) technology by combining collections of images with a set of simple visualization and analysis tools.
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BoulderALE is an RNA alignment editor, which allows for the annotation of basepairs, annotation and collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences and base composition given a secondary structure.
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Whyteboard is a painting whiteboard application for Linux and Windows, that allows the annotation of PDF and PostScript documents, and image files with common drawing tools.
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In Systems Biology models are created in various formats (Matlab, Java, C/C++, Python, ...). "Annotate Your Model" will help you to link your model to biological web resources by creating a CSV file containing MIRIAM annotations.
